Question: Annotation of org.Pf.plasmo.db out of date.
0
gravatar for lucas.michel
6 months ago by
lucas.michel0 wrote:

The annotation in the package seems out of date.

The command org.Pf.plasmo_dbInfo() shows that the plasmo.db release used is 28 while the current release is 41. I am not sure where should I ask if there is the possibility to update it.

Thank you very much,

Lucas

org.pf.plasmo.db • 134 views
ADD COMMENTlink modified 6 months ago by James W. MacDonald51k • written 6 months ago by lucas.michel0
Answer: Annotation of org.Pf.plasmo.db out of date.
0
gravatar for James W. MacDonald
6 months ago by
United States
James W. MacDonald51k wrote:

Non-model organisms like this are hard to get updated - we have limited resources as it is - so you would be better off building your own. I did this on Windows, so the call to install.packages requires a source=TRUE.

> library(AnnotationForge)
> makeOrgPackageFromNCBI("0.0.1","me <me@mine.org>","me", tax_id="36329", genus="Plasmodium",species="falciparum.3d7")
If files are not cached locally this may take awhile to assemble a 12 GB cache databse in the NCBIFilesDir directory. Subsequent calls to this function should be faster (seconds). The cache will try to rebuild once per day.
preparing data from NCBI ...
starting download for 
[1] gene2pubmed.gz
[2] gene2accession.gz
[3] gene2refseq.gz
[4] gene_info.gz
[5] gene2go.gz
getting data for gene2pubmed.gz
extracting data for our organism from : gene2pubmed
getting data for gene2accession.gz
extracting data for our organism from : gene2accession
getting data for gene2refseq.gz
extracting data for our organism from : gene2refseq
getting data for gene_info.gz
extracting data for our organism from : gene_info
getting data for gene2go.gz
extracting data for our organism from : gene2go
processing gene2pubmed
processing gene_info: chromosomes
processing gene_info: description
processing alias data
processing refseq data
processing accession data
processing GO data
Please be patient while we work out which organisms can be annotated
  with ensembl IDs.
making the OrgDb package ...
Populating genes table:
genes table filled
Populating pubmed table:
pubmed table filled
Populating chromosomes table:
chromosomes table filled
Populating gene_info table:
gene_info table filled
Populating entrez_genes table:
entrez_genes table filled
Populating alias table:
alias table filled
Populating refseq table:
refseq table filled
Populating accessions table:
accessions table filled
Populating go table:
go table filled
table metadata filled

'select()' returned many:1 mapping between keys and columns
Dropping GO IDs that are too new for the current GO.db
Populating go table:
go table filled
'select()' returned many:1 mapping between keys and columns
Populating go_all table:
go_all table filled
Creating package in c:/Users/jmacdon/Desktop/org.Pfalciparum.3d7.eg.db 

> install.packages("org.Pfalciparum.3d7.eg.db/", type = "source", repo=NULL)
Installing package into 'C:/Users/jmacdon/AppData/Roaming/R/win-library/3.5'
(as 'lib' is unspecified)
* installing *source* package 'org.Pfalciparum.3d7.eg.db' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'org.Pfalciparum.3d7.eg.db'
    finding HTML links ... done
    org.Pfalciparum 3d7.egBASE              html  
    org.Pfalciparum 3d7.egORGANISM          html  
    org.Pfalciparum 3d7.eg_dbconn           html  
** building package indices
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
* DONE (org.Pfalciparum.3d7.eg.db)
In R CMD INSTALL
> 
ADD COMMENTlink written 6 months ago by James W. MacDonald51k

Thank you very much for the reply! I'll to do it myself then.

ADD REPLYlink written 6 months ago by lucas.michel0
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